[mlpack] 206/207: Merge tag 'upstream/2.2.0'
Barak A. Pearlmutter
barak+git at pearlmutter.net
Thu Mar 23 17:53:55 UTC 2017
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bap pushed a commit to branch master
in repository mlpack.
commit 101149bcc33ff95b0c63f815587c225f62c58005
Merge: b45bcb7 40bf682
Author: Barak A. Pearlmutter <barak+git at pearlmutter.net>
Date: Thu Mar 23 15:38:25 2017 +0000
Merge tag 'upstream/2.2.0'
.travis.yml | 2 +-
CMakeLists.txt | 1 +
COPYRIGHT.txt | 14 +-
Doxyfile | 4 +-
HISTORY.md | 17 +
README.md | 16 +-
doc/guide/build.hpp | 10 +-
src/mlpack/CMakeLists.txt | 2 +-
src/mlpack/core.hpp | 9 +
src/mlpack/core/boost_backport/policy.hpp | 3 +
src/mlpack/core/data/CMakeLists.txt | 4 +
src/mlpack/core/data/binarize.hpp | 2 +-
src/mlpack/core/data/dataset_mapper.hpp | 21 +-
src/mlpack/core/data/dataset_mapper_impl.hpp | 45 +-
.../data/imputation_methods/custom_imputation.hpp | 2 +-
.../data/imputation_methods/listwise_deletion.hpp | 2 +-
.../data/imputation_methods/mean_imputation.hpp | 2 +-
.../data/imputation_methods/median_imputation.hpp | 2 +-
src/mlpack/core/data/imputer.hpp | 2 +-
src/mlpack/core/data/load.cpp | 46 ++
src/mlpack/core/data/load.hpp | 100 +++-
src/mlpack/core/data/load_arff.hpp | 2 +
src/mlpack/core/data/load_arff_impl.hpp | 13 +-
src/mlpack/core/data/load_csv.cpp | 113 ++++
src/mlpack/core/data/load_csv.hpp | 360 ++++++++++++
src/mlpack/core/data/load_impl.hpp | 253 ++------
src/mlpack/core/data/load_model_impl.hpp | 124 ++++
src/mlpack/core/data/map_policies/datatype.hpp | 2 +-
.../core/data/map_policies/increment_policy.hpp | 68 ++-
.../core/data/map_policies/missing_policy.hpp | 74 ++-
src/mlpack/core/data/split_data.hpp | 2 +-
src/mlpack/core/dists/discrete_distribution.cpp | 155 +++--
src/mlpack/core/dists/discrete_distribution.hpp | 127 +++-
src/mlpack/core/dists/gamma_distribution.cpp | 32 +-
src/mlpack/core/dists/gamma_distribution.hpp | 7 +-
src/mlpack/core/dists/gaussian_distribution.hpp | 2 +-
src/mlpack/core/dists/laplace_distribution.cpp | 2 +-
src/mlpack/core/dists/regression_distribution.hpp | 2 +-
src/mlpack/core/kernels/cosine_distance.hpp | 3 +-
src/mlpack/core/kernels/epanechnikov_kernel.hpp | 3 +-
.../core/kernels/epanechnikov_kernel_impl.hpp | 1 +
src/mlpack/core/kernels/example_kernel.hpp | 2 +-
src/mlpack/core/kernels/gaussian_kernel.hpp | 3 +-
.../core/kernels/hyperbolic_tangent_kernel.hpp | 2 +-
src/mlpack/core/kernels/laplacian_kernel.hpp | 2 +-
src/mlpack/core/kernels/linear_kernel.hpp | 2 +-
src/mlpack/core/kernels/polynomial_kernel.hpp | 2 +-
.../core/kernels/pspectrum_string_kernel.hpp | 3 +-
src/mlpack/core/kernels/spherical_kernel.hpp | 2 +-
src/mlpack/core/kernels/triangular_kernel.hpp | 2 +-
src/mlpack/core/math/columns_to_blocks.hpp | 2 +-
src/mlpack/core/math/lin_alg.cpp | 3 +-
src/mlpack/core/metrics/lmetric.hpp | 2 +-
src/mlpack/core/metrics/mahalanobis_distance.hpp | 2 +-
src/mlpack/core/optimizers/adadelta/ada_delta.hpp | 2 +-
src/mlpack/core/optimizers/adam/adam.hpp | 2 +-
.../optimizers/aug_lagrangian/aug_lagrangian.hpp | 2 +-
.../aug_lagrangian/aug_lagrangian_function.hpp | 2 +-
.../aug_lagrangian_test_functions.cpp | 43 +-
.../aug_lagrangian_test_functions.hpp | 4 +-
.../gradient_descent/gradient_descent.hpp | 2 +-
.../optimizers/gradient_descent/test_function.hpp | 2 +-
src/mlpack/core/optimizers/lbfgs/lbfgs.hpp | 2 +-
.../core/optimizers/lbfgs/test_functions.hpp | 2 +-
.../optimizers/minibatch_sgd/minibatch_sgd.hpp | 2 +-
src/mlpack/core/optimizers/rmsprop/rmsprop.hpp | 2 +-
src/mlpack/core/optimizers/sdp/lrsdp.hpp | 2 +-
src/mlpack/core/optimizers/sdp/lrsdp_function.hpp | 2 +-
src/mlpack/core/optimizers/sdp/primal_dual.hpp | 2 +-
src/mlpack/core/optimizers/sdp/sdp.hpp | 3 +-
src/mlpack/core/optimizers/sgd/sgd.hpp | 2 +-
src/mlpack/core/optimizers/sgd/test_function.hpp | 2 +-
src/mlpack/core/tree/ballbound.hpp | 2 +-
src/mlpack/core/tree/ballbound_impl.hpp | 1 +
src/mlpack/core/tree/binary_space_tree.hpp | 2 +-
.../tree/binary_space_tree/binary_space_tree.hpp | 2 +-
.../breadth_first_dual_tree_traverser.hpp | 2 +-
.../tree/binary_space_tree/dual_tree_traverser.hpp | 2 +-
.../core/tree/binary_space_tree/mean_split.hpp | 2 +-
.../core/tree/binary_space_tree/midpoint_split.hpp | 2 +-
.../tree/binary_space_tree/rp_tree_max_split.hpp | 2 +-
.../tree/binary_space_tree/rp_tree_mean_split.hpp | 3 +-
.../binary_space_tree/single_tree_traverser.hpp | 2 +-
.../core/tree/binary_space_tree/ub_tree_split.hpp | 2 +-
.../tree/binary_space_tree/vantage_point_split.hpp | 3 +-
src/mlpack/core/tree/cellbound.hpp | 2 +-
src/mlpack/core/tree/cosine_tree/cosine_tree.cpp | 1 +
src/mlpack/core/tree/cosine_tree/cosine_tree.hpp | 2 +-
src/mlpack/core/tree/cover_tree.hpp | 2 +-
src/mlpack/core/tree/cover_tree/cover_tree.hpp | 3 +-
.../core/tree/cover_tree/dual_tree_traverser.hpp | 2 +-
.../tree/cover_tree/dual_tree_traverser_impl.hpp | 2 +-
.../core/tree/cover_tree/first_point_is_root.hpp | 2 +-
.../core/tree/cover_tree/single_tree_traverser.hpp | 2 +-
.../core/tree/greedy_single_tree_traverser.hpp | 2 +-
src/mlpack/core/tree/hollow_ball_bound.hpp | 2 +-
src/mlpack/core/tree/hrectbound.hpp | 2 +-
src/mlpack/core/tree/octree.hpp | 2 +-
.../core/tree/octree/dual_tree_traverser.hpp | 2 +-
src/mlpack/core/tree/octree/octree.hpp | 2 +-
.../core/tree/octree/single_tree_traverser.hpp | 2 +-
.../tree/rectangle_tree/discrete_hilbert_value.hpp | 2 +-
.../tree/rectangle_tree/dual_tree_traverser.hpp | 2 +-
.../hilbert_r_tree_descent_heuristic.hpp | 2 +-
.../tree/rectangle_tree/hilbert_r_tree_split.hpp | 2 +-
.../r_plus_plus_tree_auxiliary_information.hpp | 2 +-
.../r_plus_plus_tree_descent_heuristic.hpp | 2 +-
.../r_plus_tree_descent_heuristic.hpp | 2 +-
.../r_plus_tree_descent_heuristic_impl.hpp | 2 +-
.../core/tree/rectangle_tree/r_plus_tree_split.hpp | 2 +-
.../r_star_tree_descent_heuristic.hpp | 2 +-
.../core/tree/rectangle_tree/r_star_tree_split.hpp | 2 +-
.../rectangle_tree/r_tree_descent_heuristic.hpp | 2 +-
.../core/tree/rectangle_tree/r_tree_split.hpp | 2 +-
.../core/tree/rectangle_tree/rectangle_tree.hpp | 2 +-
.../tree/rectangle_tree/single_tree_traverser.hpp | 2 +-
.../core/tree/rectangle_tree/x_tree_split.hpp | 2 +-
src/mlpack/core/tree/space_split/hyperplane.hpp | 2 +-
.../core/tree/space_split/mean_space_split.hpp | 2 +-
.../core/tree/space_split/midpoint_space_split.hpp | 2 +-
.../core/tree/space_split/projection_vector.hpp | 2 +-
src/mlpack/core/tree/space_split/space_split.hpp | 2 +-
src/mlpack/core/tree/spill_tree.hpp | 2 +-
.../tree/spill_tree/spill_dual_tree_traverser.hpp | 2 +-
.../spill_tree/spill_single_tree_traverser.hpp | 2 +-
src/mlpack/core/tree/spill_tree/spill_tree.hpp | 2 +-
src/mlpack/core/util/backtrace.cpp | 1 -
src/mlpack/core/util/cli.hpp | 2 +
src/mlpack/core/util/param.hpp | 2 +
src/mlpack/core/util/prefixedoutstream.cpp | 7 +-
src/mlpack/core/util/prefixedoutstream.hpp | 32 +-
src/mlpack/core/util/prefixedoutstream_impl.hpp | 139 ++++-
src/mlpack/core/util/singletons.cpp | 4 +-
src/mlpack/core/util/singletons.hpp | 2 +-
src/mlpack/core/util/version.hpp | 8 +-
src/mlpack/methods/CMakeLists.txt | 4 +-
src/mlpack/methods/adaboost/adaboost.hpp | 2 +-
src/mlpack/methods/adaboost/adaboost_main.cpp | 6 +-
src/mlpack/methods/amf/amf.hpp | 2 +-
src/mlpack/methods/amf/init_rules/average_init.hpp | 2 +-
src/mlpack/methods/amf/init_rules/given_init.hpp | 2 +-
.../methods/amf/init_rules/random_acol_init.hpp | 3 +-
src/mlpack/methods/amf/init_rules/random_init.hpp | 2 +-
.../incomplete_incremental_termination.hpp | 2 +-
.../simple_residue_termination.hpp | 2 +-
.../simple_tolerance_termination.hpp | 2 +-
.../validation_RMSE_termination.hpp | 2 +-
src/mlpack/methods/amf/update_rules/nmf_als.hpp | 2 +-
.../methods/amf/update_rules/nmf_mult_dist.hpp | 2 +-
.../methods/amf/update_rules/nmf_mult_div.hpp | 2 +-
.../amf/update_rules/svd_batch_learning.hpp | 2 +-
.../svd_complete_incremental_learning.hpp | 2 +-
src/mlpack/methods/approx_kfn/approx_kfn_main.cpp | 4 +-
src/mlpack/methods/approx_kfn/drusilla_select.hpp | 2 +-
src/mlpack/methods/approx_kfn/qdafn.hpp | 3 +-
src/mlpack/methods/cf/cf.hpp | 2 +-
src/mlpack/methods/cf/cf_main.cpp | 14 +-
src/mlpack/methods/cf/svd_wrapper.hpp | 2 +-
src/mlpack/methods/dbscan/CMakeLists.txt | 18 +
src/mlpack/methods/dbscan/dbscan.hpp | 157 +++++
src/mlpack/methods/dbscan/dbscan_impl.hpp | 184 ++++++
src/mlpack/methods/dbscan/dbscan_main.cpp | 149 +++++
.../methods/dbscan/random_point_selection.hpp | 58 ++
.../methods/decision_stump/decision_stump.hpp | 19 +-
.../methods/decision_stump/decision_stump_impl.hpp | 19 +
.../methods/decision_stump/decision_stump_main.cpp | 6 +-
src/mlpack/methods/decision_tree/CMakeLists.txt | 25 +
.../decision_tree/all_categorical_split.hpp | 96 +++
.../decision_tree/all_categorical_split_impl.hpp | 101 ++++
.../decision_tree/best_binary_numeric_split.hpp | 93 +++
.../best_binary_numeric_split_impl.hpp | 103 ++++
src/mlpack/methods/decision_tree/decision_tree.hpp | 288 +++++++++
.../methods/decision_tree/decision_tree_impl.hpp | 642 +++++++++++++++++++++
.../methods/decision_tree/decision_tree_main.cpp | 216 +++++++
src/mlpack/methods/decision_tree/gini_gain.hpp | 80 +++
.../methods/decision_tree/information_gain.hpp | 78 +++
src/mlpack/methods/det/det_main.cpp | 5 +-
src/mlpack/methods/det/dt_utils.hpp | 2 +-
src/mlpack/methods/det/dtree.hpp | 2 +-
src/mlpack/methods/emst/dtb.hpp | 2 +-
src/mlpack/methods/emst/dtb_rules.hpp | 2 +-
src/mlpack/methods/emst/dtb_stat.hpp | 2 +-
src/mlpack/methods/emst/edge_pair.hpp | 2 +-
src/mlpack/methods/emst/emst_main.cpp | 4 +-
src/mlpack/methods/emst/union_find.hpp | 2 +-
src/mlpack/methods/fastmks/fastmks.hpp | 2 +-
src/mlpack/methods/fastmks/fastmks_main.cpp | 5 +-
src/mlpack/methods/fastmks/fastmks_model.hpp | 13 +-
src/mlpack/methods/fastmks/fastmks_rules.hpp | 3 +-
src/mlpack/methods/fastmks/fastmks_stat.hpp | 2 +-
src/mlpack/methods/gmm/diagonal_constraint.hpp | 2 +-
.../methods/gmm/eigenvalue_ratio_constraint.hpp | 2 +-
src/mlpack/methods/gmm/em_fit.hpp | 3 +-
src/mlpack/methods/gmm/gmm.hpp | 2 +-
src/mlpack/methods/gmm/gmm_generate_main.cpp | 4 +-
src/mlpack/methods/gmm/gmm_probability_main.cpp | 4 +-
src/mlpack/methods/gmm/gmm_train_main.cpp | 4 +-
src/mlpack/methods/gmm/no_constraint.hpp | 2 +-
.../methods/gmm/positive_definite_constraint.hpp | 2 +-
src/mlpack/methods/hmm/hmm.hpp | 3 +-
src/mlpack/methods/hmm/hmm_generate_main.cpp | 4 +-
src/mlpack/methods/hmm/hmm_loglik_main.cpp | 4 +-
src/mlpack/methods/hmm/hmm_regression.hpp | 2 +-
src/mlpack/methods/hmm/hmm_train_main.cpp | 144 ++++-
src/mlpack/methods/hmm/hmm_util.hpp | 2 +-
src/mlpack/methods/hmm/hmm_util_impl.hpp | 2 +-
src/mlpack/methods/hmm/hmm_viterbi_main.cpp | 4 +-
.../hoeffding_trees/binary_numeric_split_info.hpp | 2 +-
.../hoeffding_trees/categorical_split_info.hpp | 2 +-
.../methods/hoeffding_trees/gini_impurity.hpp | 2 +-
.../hoeffding_categorical_split.hpp | 2 +-
.../hoeffding_trees/hoeffding_numeric_split.hpp | 2 +-
.../methods/hoeffding_trees/hoeffding_tree.hpp | 3 +-
.../hoeffding_trees/hoeffding_tree_main.cpp | 5 +-
.../methods/hoeffding_trees/numeric_split_info.hpp | 2 +-
src/mlpack/methods/kernel_pca/kernel_pca.hpp | 2 +-
src/mlpack/methods/kernel_pca/kernel_pca_main.cpp | 18 +-
.../kernel_pca/kernel_rules/naive_method.hpp | 2 +-
.../kernel_pca/kernel_rules/nystroem_method.hpp | 2 +-
src/mlpack/methods/kmeans/allow_empty_clusters.hpp | 2 +-
src/mlpack/methods/kmeans/kill_empty_clusters.hpp | 2 +-
src/mlpack/methods/kmeans/kmeans.hpp | 2 +-
src/mlpack/methods/kmeans/kmeans_main.cpp | 4 +-
.../methods/kmeans/max_variance_new_cluster.hpp | 2 +-
src/mlpack/methods/kmeans/random_partition.hpp | 2 +-
src/mlpack/methods/kmeans/refined_start.hpp | 2 +-
.../methods/kmeans/sample_initialization.hpp | 3 +-
src/mlpack/methods/lars/lars.cpp | 2 +
src/mlpack/methods/lars/lars.hpp | 2 +-
src/mlpack/methods/lars/lars_main.cpp | 5 +-
.../linear_regression/linear_regression.cpp | 1 +
.../linear_regression/linear_regression.hpp | 2 +-
.../linear_regression/linear_regression_main.cpp | 5 +-
src/mlpack/methods/local_coordinate_coding/lcc.cpp | 1 +
src/mlpack/methods/local_coordinate_coding/lcc.hpp | 2 +-
.../local_coordinate_coding_main.cpp | 5 +-
.../logistic_regression/logistic_regression.hpp | 8 +-
.../logistic_regression_function.hpp | 2 +-
.../logistic_regression_main.cpp | 5 +-
src/mlpack/methods/lsh/lsh_main.cpp | 5 +-
src/mlpack/methods/lsh/lsh_search.hpp | 2 +-
src/mlpack/methods/lsh/lsh_search_impl.hpp | 3 +-
src/mlpack/methods/mean_shift/mean_shift.hpp | 2 +-
src/mlpack/methods/mean_shift/mean_shift_main.cpp | 5 +-
.../methods/naive_bayes/naive_bayes_classifier.hpp | 2 +-
.../naive_bayes/naive_bayes_classifier_impl.hpp | 2 +-
src/mlpack/methods/naive_bayes/nbc_main.cpp | 8 +-
src/mlpack/methods/nca/nca.hpp | 2 +-
src/mlpack/methods/nca/nca_main.cpp | 7 +-
.../methods/nca/nca_softmax_error_function.hpp | 2 +-
src/mlpack/methods/neighbor_search/kfn_main.cpp | 4 +-
src/mlpack/methods/neighbor_search/knn_main.cpp | 6 +-
.../methods/neighbor_search/neighbor_search.hpp | 13 +-
.../neighbor_search/neighbor_search_impl.hpp | 64 +-
.../neighbor_search/neighbor_search_stat.hpp | 2 +-
.../sort_policies/furthest_neighbor_sort.hpp | 2 +-
.../sort_policies/nearest_neighbor_sort.hpp | 2 +-
src/mlpack/methods/neighbor_search/unmap.hpp | 2 +-
src/mlpack/methods/nmf/nmf_main.cpp | 5 +-
.../methods/nystroem_method/kmeans_selection.hpp | 2 +-
.../methods/nystroem_method/nystroem_method.hpp | 2 +-
.../methods/nystroem_method/ordered_selection.hpp | 2 +-
.../methods/nystroem_method/random_selection.hpp | 2 +-
.../decomposition_policies/exact_svd_method.hpp | 2 +-
.../pca/decomposition_policies/quic_svd_method.hpp | 2 +-
.../randomized_svd_method.hpp | 2 +-
src/mlpack/methods/pca/pca.hpp | 2 +-
src/mlpack/methods/pca/pca_impl.hpp | 3 +-
src/mlpack/methods/pca/pca_main.cpp | 5 +-
.../initialization_methods/random_init.hpp | 2 +-
.../initialization_methods/zero_init.hpp | 2 +-
.../learning_policies/simple_weight_update.hpp | 2 +-
src/mlpack/methods/perceptron/perceptron.hpp | 2 +-
src/mlpack/methods/perceptron/perceptron_main.cpp | 16 +-
.../preprocess/preprocess_binarize_main.cpp | 5 +-
.../preprocess/preprocess_describe_main.cpp | 5 +-
.../methods/preprocess/preprocess_imputer_main.cpp | 7 +-
.../methods/preprocess/preprocess_split_main.cpp | 14 +-
src/mlpack/methods/quic_svd/quic_svd.cpp | 2 +-
src/mlpack/methods/quic_svd/quic_svd.hpp | 2 +-
src/mlpack/methods/radical/radical.cpp | 2 +
src/mlpack/methods/radical/radical.hpp | 2 +-
src/mlpack/methods/radical/radical_main.cpp | 6 +-
.../methods/randomized_svd/randomized_svd.cpp | 2 +-
.../methods/randomized_svd/randomized_svd.hpp | 2 +-
src/mlpack/methods/range_search/range_search.hpp | 17 +-
.../methods/range_search/range_search_impl.hpp | 61 ++
.../methods/range_search/range_search_main.cpp | 4 +-
.../methods/range_search/range_search_stat.hpp | 2 +-
src/mlpack/methods/range_search/rs_model.cpp | 350 +----------
src/mlpack/methods/range_search/rs_model.hpp | 269 +++++++--
src/mlpack/methods/range_search/rs_model_impl.hpp | 412 ++++++-------
src/mlpack/methods/rann/krann_main.cpp | 4 +-
src/mlpack/methods/rann/ra_model_impl.hpp | 1 +
src/mlpack/methods/rann/ra_query_stat.hpp | 2 +-
src/mlpack/methods/rann/ra_search.hpp | 2 +-
src/mlpack/methods/rann/ra_search_impl.hpp | 2 +-
src/mlpack/methods/rann/ra_util.hpp | 2 +-
.../methods/regularized_svd/regularized_svd.hpp | 2 +-
.../regularized_svd/regularized_svd_function.hpp | 2 +-
.../softmax_regression/softmax_regression.hpp | 27 +-
.../softmax_regression_function.hpp | 2 +-
.../softmax_regression/softmax_regression_impl.hpp | 26 +-
.../softmax_regression/softmax_regression_main.cpp | 13 +-
.../methods/sparse_autoencoder/maximal_inputs.hpp | 2 +-
.../sparse_autoencoder/sparse_autoencoder.hpp | 2 +-
.../sparse_autoencoder_function.hpp | 2 +-
.../data_dependent_random_initializer.hpp | 3 +-
.../methods/sparse_coding/nothing_initializer.hpp | 2 +-
.../methods/sparse_coding/random_initializer.hpp | 2 +-
src/mlpack/methods/sparse_coding/sparse_coding.cpp | 2 +
src/mlpack/methods/sparse_coding/sparse_coding.hpp | 2 +-
.../methods/sparse_coding/sparse_coding_main.cpp | 5 +-
src/mlpack/prereqs.hpp | 13 +
src/mlpack/tests/CMakeLists.txt | 2 +
src/mlpack/tests/data/casecheck.arff | 16 +
src/mlpack/tests/dbscan_test.cpp | 149 +++++
src/mlpack/tests/decision_tree_test.cpp | 601 +++++++++++++++++++
src/mlpack/tests/distribution_test.cpp | 370 +++++++++++-
src/mlpack/tests/gmm_test.cpp | 25 +-
src/mlpack/tests/hmm_test.cpp | 14 +-
src/mlpack/tests/hoeffding_tree_test.cpp | 80 +--
src/mlpack/tests/imputation_test.cpp | 1 +
src/mlpack/tests/lars_test.cpp | 1 +
src/mlpack/tests/load_save_test.cpp | 279 +++++++--
src/mlpack/tests/mlpack_test.cpp | 4 +-
src/mlpack/tests/perceptron_test.cpp | 85 +++
src/mlpack/tests/prefixedoutstream_test.cpp | 79 +++
src/mlpack/tests/range_search_test.cpp | 71 ++-
src/mlpack/tests/serialization_test.cpp | 43 +-
src/mlpack/tests/test_tools.hpp | 28 +
331 files changed, 6669 insertions(+), 1458 deletions(-)
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